Katherine Archuleta had come under criticism after revelations that the hack, which many suspect originated in China, affected a staggering 21.5 million people, far more than initially believed.
The data breach swept up Social Security numbers and other information about current and former government workers, applicants, contractors and spouses of those who underwent background checks for security clearances.
"I conveyed to the president that I believe it is best for me to step aside and allow new leadership to step in, enabling the agency to move beyond the current challenges," said Archuleta, who had been in the post since November 2013.
Beth Cobert will from Saturday assume the role of acting OPM director, the official said.
Also Read
Outrage has been growing in Washington and among federal workers over the breach, an incident which puts officials in a quandary over dealing with China, the main suspect in the attack. Beijing insists it had nothing to do with the hack.
Democratic US Senator Barbara Mikulski called the hack "as outrageous and unacceptable as it is devastating."
"This erodes confidence going forward that the federal government will be able to protect federal employees," she said.
The National Treasury Employees Union, which has sued over the breach, said the government's offer of three years of fraud monitoring was woefully inadequate.
The union "continues to be outraged that so many of our members have had their personal information compromised due to these breaches," union president Colleen Kelley said.
"We will continue to pursue our lawsuit to provide lifetime credit monitoring and identity theft protection.